So when you use the Emergency Action Card, it comes back upside down. How do I flip it over? I can't find that in the rules, so I assume it's an asset card, but I don't want to miss this if its buried in the rule book somewhere.

There is a regular action card that one of the choices allows you to flip it back over.

I am not going to dig through my set to find it, but its there.

Yeah the action card is called Full Deployment I believe, its a security card.